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Sherwin J Singer

Publications and source records attributed to Sherwin J Singer.

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A reexamination of the ice III/IX hydrogen bond ordering phase transition.

Ice III is a hydrogen bond disordered crystal which when cooled 1 K / min or faster transforms to an antiferroelectric hydrogen bond ordered structure, ice IX. Throughout its region of stability, experiments indicate that the H bonds in ice III are, in fact, partially ordered, i.e., some proton arrangements are preferred. In addition, there has been evidence that the structure of ice IX retains some residual disorder after the transition. Diffraction experiments and calorimetry apparently conflict with regard to the degree of ordering at the ice III/IX transition. Mean field statistical mechanical theories have been used to link partial occupations from diffraction data with thermodynamics. In this work, we investigate the ice III/IX proton ordering phase transition using electronic density functional theory calculations for small unit cells, extended to simulate the phase transition in a large unit cell using graph invariants. In agreement with experiment, we observe partial ordering over a wide range of temperatures as ice III transforms to partially disordered ice IX, near 126 K, which becomes fully ordered at lower temperatures. We compare our results from full statistical mechanical simulations with mean field models, finding small errors for the low-temperature ice IX phase and much larger errors for the high-temperature ice III phase. The failure of mean field theories may explain the apparent conflict between diffraction experiments and calorimetry.

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A molecular dynamics study of Lys-Trp-Lys: structure and dynamics in solution following photoexcitation.

We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three protonated amino groups and the indole moiety. For the excited state of tryptophan in KWK, the simulated molecular dynamics of the three isomers are similar, all in good agreement with recent femtosecond experiments (J. Phys. Chem. B 2005, 109, 16901). Specifically, we observe: (1) the fluorescence anisotropy is dominated by a single-exponential component and decays in approximately 130 ps, (2) the total dynamic Stokes shift reaches approximately 2700 cm(-1), and (3) the excited state relaxation dynamics occurs on several time scales ranging from femtoseconds to tens of picoseconds. The relaxation dynamics involve rapid initial response of neighboring water, followed by local motions of flexible peptide chains. These processes drive global restructuring of the tripeptide on a rather flat energy surface, inducing slower dynamics evident in both the water and protein contributions to the stabilization energy of the photoexcited chromophore. The water and protein dynamics are strongly correlated. On a still longer time scale, we observe isomerization of two excited state conformers to the other most stable one, an analogue for evolution of trajectories along the funnel on the rugged free energy landscape to the final "native" state. Our studies suggest new experiments to detect this unique dynamics.

Isomerism↗

Hydrogen bond topology and the ice VII/VIII and Ih/XI proton ordering phase transitions.

Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled under special conditions is believed to transform to ferroelectric proton-ordered ice XI, but this transformation is still subject to controversy. Ice VII, also proton disordered throughout its region of stability, transforms to proton-ordered ice VIII upon cooling. In contrast to the ice Ih/XI transition, the VII/VIII transition and the crystal structure of ice VIII are well characterized. In order to shed some light on the ice Ih proton ordering transition, we present the results of periodic electronic density functional theory calculations and statistical simulations. We are able to describe the small energy differences among the innumerable H-bond configurations possible in a large simulation cell by using an analytic theory to extrapolate from electronic DFT calculations on small unit cells to cells large enough to approximate the thermodynamic limit. We first validate our methods by comparing our predictions to the well-characterized ice VII/VIII proton ordering transition, finding agreement with respect to both the transition temperature and structure of the low-temperature phase. For ice Ih, our results indicate that a proton-ordered phase is attainable at low temperatures, the structure of which is in agreement with the experimentally proposed ferroelectric structure. The predicted transition temperature of is in qualitative agreement with the observed transition at on KOH-doped ice samples.

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Prediction of a phase transition to a hydrogen bond ordered form of ice VI.

Ice VI is a hydrogen bond disordered crystal over its known region of stability. In this work, we predict that ice VI will transform into a hydrogen bond ordered phase near 108 K, and have identified the likely low-temperature phase as ferroelectric (space group Cc) with an antiferroelectric structure (space group P2(1)2(1)2(1)) close by in energy. Electronic density functional theory calculations provide input to our calculations, which are extended to cells large enough for statistical simulations by using graph invariants. A significant decrease in the configurational entropy is predicted as hydrogen bonds exhibit partial order above the transition, provided that the hydrogen bonds can equilibrate on an experimental time scale. Conversely, partial disorder is predicted at temperatures below the transition. Although some evidence for ordering of ice VI has been observed in experiments, a low-temperature proton ordered phase has not been identified experimentally.

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Electro-osmotic flow of a model electrolyte.

Electro-osmotic flow is studied by nonequilibrium molecular dynamics simulations in a model system chosen to elucidate various factors affecting the velocity profile and facilitate comparison with existing continuum theories. The model system consists of spherical ions and solvent, with stationary, uniformly charged walls that make a channel with a height of 20 particle diameters. We find that hydrodynamic theory adequately describes simple pressure-driven (Poiseuille) flow in this model. However, Poisson-Boltzmann theory fails to describe the ion distribution in important situations, and therefore continuum fluid dynamics based on the Poisson-Boltzmann ion distribution disagrees with simulation results in those situations. The failure of Poisson-Boltzmann theory is traced to the exclusion of ions near the channel walls resulting from reduced solvation of the ions in that region. When a corrected ion distribution is used as input for hydrodynamic theory, agreement with numerical simulations is restored. An analytic theory is presented that demonstrates that repulsion of the ions from the channel walls increases the flow rate, and attraction to the walls has the opposite effect. A recent numerical study of electro-osmotic flow is reanalyzed in the light of our findings, and the results conform well to our conclusions for the model system.

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Hydrogen-bond topology and the ice VII/VIII and ice Ih/XI proton-ordering phase transitions.

The existence of an ice Ih/XI proton-ordering transition to a low-temperature ferroelectric phase has sparked considerable debate in the literature. Electronic density functional theory calculations, extended using graph invariants, confirm that a transition to a low-temperature ferroelectric phase should occur. The predicted transition at 98 K is in qualitative agreement with the observed transition at 72 K, and the low-temperature phase is the ferroelectric phase determined in diffraction experiments. The theoretical methods used to predict the phase transition are validated by comparing their prediction to the well-characterized ice VII/VIII proton-ordering transition.

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Graph invariants for periodic systems: towards predicting physical properties from the hydrogen bond topology of ice.

Ice-Ih consists of a disordered hydrogen-bonded network. The degree of disorder in ice-Ih, and possible phase transitions to an ordered phase have been debated in recent years. The dependence of energy, free energy, and other scalar physical properties on H-bond topology is needed to understand these phenomena. Graph invariants provide a means of linking physical properties to the topology of the H-bond network. We have previously shown the effectiveness of graph invariants for finite water clusters [J.-L. Kuo, J. V. Coe, S. J. Singer, Y. B. Band, and L. Ojamäe, J. Chem. Phys., 114, 2527 (2001)]. In this work, we develop a formalism for the graph invariants of periodic systems. We demonstrate that graph invariants for small unit cells are a subset of the graph invariants of larger unit cells, providing a hierarchy of approximations by which detailed calculations for small unit cells, such as periodic ab initio calculations as they become available, can be used to parametrize the energy of the astronomical number of H-bond arrangements present in large unit cells. We also present graph enumeration results for ice-Ih, analyzing conflicting results that have appeared previously in the literature and furnishing information on the statistical properties of the H-bond network of ice-Ih in the large system limit.

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Computer simulations of a two-dimensional system with competing interactions.

The results and methodology of large scale computer simulations of the two-dimensional dipolar Ising model with long-range interactions are reported. Systems as large as 117,649 particles were studied to elucidate the elementary excitations and phase diagram of two-dimensional systems, such as Langmuir monolayers, thin garnet films, and adsorbed films on solid surfaces, which spontaneously form patterns of stripes, bubbles, and intermediately shaped domains. The challenging numerical investigations of large scale systems with long-range interactions at low temperatures were made possible by combining the fast multipole method and a non-Metropolis Monte Carlo sampling technique. Our simulations provide evidence that, at sufficiently high ratios of the repulsive to the attractive coupling constant for the model, twofold stripe order in the systems of interest is lost through a defect-mediated mechanism. Heat capacity data and the excitations observed in our simulations as the system disorders indicate that it is most likely an instance of a Kosterlitz-Thouless phase transition. The results from simulations with and without external field are in excellent agreement with the predictions of an analytic scaling theory [A. D. Stoycheva and S. J. Singer, Phys. Rev. E 64, 016118 (2001)], confirming the phase diagram furnished by the analytic model. The scaling theory suggests that, under certain conditions, defect-mediated stripe melting may be supplanted by Ising like disordering within stripes for small repulsion strength. A qualitative discussion of a model that supports both disordering mechanisms is presented.

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